Very good subject. I too always round up when I personally shop and think, "Why don't they just round up." Do they think I don't know that $24.99 is really $25. (Giggle).
But now on the other hand, after I have done all my calculations and the item come out to be $13.00 I will charge $12.95. Why? The number 13 is unsettling to some people (not me) and I just think $12.95 looks better.
Also when I'm in say my Pay Pal account I can just look at the figures and know what item the customer had bought.
Bottom line is, "Round up" before you ".99", your customers will like it better and it is easier to add up at a glance. But on the other hand if your gut is telling you to go with a .99 then go with it.
Hope this has helped.
My best to all
Lisa Marie